The CDC estimates that over 73,000 cases of E. coli O157:H7 infections occur annually in the US, but the pathogenesis of E. coli O157:H7 is poorly understood. The first step in gastro-intestinal disease is colonization, yet despite extensive research next to nothing is known about this process. To colonize the intestinal tract, E. coli O157:H7 must survive the hostile acidic pH of the gastric contents, pass through the small intestine, adhere to the colonic intestinal epithelium, adapt to the colonic environment, and acquire essential nutrients for growth. The same is true for the 400-500 commensal species that inhabit the mammalian large intestine and again, next to nothing is known about this process. For the last few years, we have used colonization by commensal E. coli strains as a model and are beginning to understand the process better. Mucus provides the nutrients necessary for commensal E. coli strains to colonize. Our results substantiate the essential role of mucus-derived sugar acids-hexonic and neuronic acids-for intestinal colonization by E. coli and stand in contrast to widely held, yet unchallenged assumption that glucose is the major carbon source available to microbial invaders- but there is essentially no free glucose in the colon. Our improved understanding of colonization came as we began to use functional genomics tools for examining E. coli metabolism during in vitro growth and intestinal colonization by commensal strains to include a pathogen. We will develop functional genomic tools to understand the in situ physiology of E. coli O157:H7, and thus illuminate the process by which intestinal pathogens first colonize a host.